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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11196 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2014-01-08 20:47:11 +00:00
parent 5147d86b98
commit 16652ef654
2 changed files with 9 additions and 3 deletions
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6
src/create_atoms.cpp
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@ -429,7 +429,7 @@ void CreateAtoms::add_single()
coord = lamda; coord = lamda;
} else coord = xone; } else coord = xone;
// if atom is in my subbox, create it // if atom/molecule is in my subbox, create it
if (coord[0] >= sublo[0] && coord[0] < subhi[0] && if (coord[0] >= sublo[0] && coord[0] < subhi[0] &&
coord[1] >= sublo[1] && coord[1] < subhi[1] && coord[1] >= sublo[1] && coord[1] < subhi[1] &&
@ -481,7 +481,7 @@ void CreateAtoms::add_random()
zhi = MIN(zhi,domain->regions[nregion]->extent_zhi); zhi = MIN(zhi,domain->regions[nregion]->extent_zhi);
} }
// generate random positions for each new atom within bounding box // generate random positions for each new atom/molecule within bounding box
// iterate until atom is within region and triclinic simulation box // iterate until atom is within region and triclinic simulation box
// if final atom position is in my subbox, create it // if final atom position is in my subbox, create it
@ -615,7 +615,7 @@ void CreateAtoms::add_lattice()
if (style == REGION) if (style == REGION)
if (!domain->regions[nregion]->match(x[0],x[1],x[2])) continue; if (!domain->regions[nregion]->match(x[0],x[1],x[2])) continue;
// test if atom is in my subbox // test if atom/molecule position is in my subbox
if (triclinic) { if (triclinic) {
domain->x2lamda(x,lamda); domain->x2lamda(x,lamda);

6
src/force.cpp
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@ -568,6 +568,12 @@ void Force::set_special(int narg, char **arg)
{ {
if (narg == 0) error->all(FLERR,"Illegal special_bonds command"); if (narg == 0) error->all(FLERR,"Illegal special_bonds command");
// defaults
special_lj[1] = special_lj[2] = special_lj[3] = 0.0;
special_coul[1] = special_coul[2] = special_coul[3] = 0.0;
special_angle = special_dihedral = special_extra = 0;
int iarg = 0; int iarg = 0;
while (iarg < narg) { while (iarg < narg) {
if (strcmp(arg[iarg],"amber") == 0) { if (strcmp(arg[iarg],"amber") == 0) {